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    43 repositories

    • SplitMEM_BWT

      Public
      SplitMEM submodule for deMEM
      C++
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • sdsl-lite-all-in-one

      Public
      Parallel suffix array calculation, used in SplitMEM
      C++
      •1•0•0•0•Updated Mar 11, 2025Mar 11, 2025

    • subhalign3

      Public
      HAlign 3 for deMEM
      Batchfile
      •1•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • submafft

      Public
      MAFFT Submodule for deMEM
      Shell
      •1•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • msawebsite

      Public
      website sources
      HTML
      •5•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • RaMA

      Public
      Fast sequence alignment for centromere with RaMA
      C++
      •
      Apache License 2.0
      •1•3•0•0•Updated Jan 31, 2025Jan 31, 2025

    • HAlign-4

      Public
      HAlign 4: A New Strategy for Rapidly Aligning Millions of Sequences
      C++
      •
      MIT License
      •2•4•0•0•Updated Jan 8, 2025Jan 8, 2025

    • FORAlign_testcase

      Public
      Test Data For FORAlign
      1•0•0•0•Updated Dec 30, 2024Dec 30, 2024

    • ReAlign-N

      Public
      🧬ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments
      multiple-sequence-alignmentrealignment
      C++
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Dec 25, 2024Dec 25, 2024

    • HAlign-G

      Public
      A rapid and low-memory multiple-genome aligner for thousands of human genomes
      C
      •
      MIT License
      •0•4•0•0•Updated Nov 7, 2024Nov 7, 2024

    • FORAlign

      Public
      FORAlign: Accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on FOur Russians approach with linear space complexity
      C
      •2•1•0•0•Updated Nov 5, 2024Nov 5, 2024

    • ReAlign-Star

      Public
      🌟ReAlign-Star: an optimized realignment method for multiple sequence alignment, targeting star algorithm tools
      C++
      •
      MIT License
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • Chimera

      Public
      Chimera: A Versatile Metagenomic Classification Tool
      C
      •
      MIT License
      •2•2•0•0•Updated Oct 11, 2024Oct 11, 2024

    • klib

      Public
      klib的代码以及部分教程
      C
      •1•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • MSATOOLS

      Public
      C++
      •3•5•0•0•Updated Jun 19, 2024Jun 19, 2024

    • SSW

      Public
      Complete Striped Smith Waterman Library with Windows & Linux
      C
      •119•0•0•0•Updated Jun 17, 2024Jun 17, 2024

    • TPMA

      Public
      ⚙️TPMA: a two pointers meta-alignment tool to ensemble different nucleic acid multiple sequence alignment results
      refinementmultiple-sequence-alignmentmeta-alignment
      C++
      •
      MIT License
      •0•7•0•0•Updated Apr 9, 2024Apr 9, 2024

    • staccato

      Public
      C++11 Work-Stealing Task Scheduler
      C++
      •
      MIT License
      •3•0•0•0•Updated Apr 2, 2024Apr 2, 2024

    • FMAlign2

      Public
      FMAlign2: A novel fast multiple nucleotide sequence alignment method for ultra-long datasets
      C++
      •
      Apache License 2.0
      •2•6•0•0•Updated Jan 22, 2024Jan 22, 2024

    • HIV-data

      Public
      HIV sequence data which stored separately according to sequence length
      0•0•0•0•Updated Dec 28, 2023Dec 28, 2023

    • GMGC-data

      Public
      Global Microbial Gene Catalog sequence data which stored separately according to sequence length
      0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • HAlign-G-data

      Public
      A rapid and low-memory multiple-genome aligner for thousands of human genomes
      MIT License
      •0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • abPOA

      Public
      abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
      C
      •
      MIT License
      •18•1•0•0•Updated Aug 22, 2023Aug 22, 2023

    • MPoxVR_dataset

      Public
      MPox Virus sequence dataset
      Jupyter Notebook
      •1•0•0•0•Updated Aug 19, 2023Aug 19, 2023

    • stmsa-cpp

      Public
      do multiple nucleotide sequence alignment fast and accurately
      suffix-treemultiple-sequence-alignmentcpp
      C++
      •
      MIT License
      •1•3•0•0•Updated Jul 11, 2023Jul 11, 2023

    • mafft-twomodule

      Public
      This is a part of other programs.
      C
      •
      Other
      •1•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • QuanTest2

      Public
      QuanTest2 using Q Score and TC Score
      Shell
      •1•0•0•0•Updated Jun 27, 2023Jun 27, 2023

    • WMSA2

      Public
      fast alignment for large RNA/DNA datasets
      sequence-alignmentmsa
      Java
      •
      MIT License
      •0•1•1•0•Updated Jun 21, 2023Jun 21, 2023

    • qscore

      Public
      Compares a multiple alignment with a reference and reports accuracy scores.
      C
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Apr 19, 2023Apr 19, 2023

    • parallel-suffixArray

      Public
      parallel suffix Array implementation: parallel DC3 & ParallelRange
      C++
      •1•0•0•0•Updated Mar 9, 2023Mar 9, 2023